2024-05-22T08:42:32,092 Created temporary directory: /tmp/pip-build-tracker-_na853u_ 2024-05-22T08:42:32,094 Initialized build tracking at /tmp/pip-build-tracker-_na853u_ 2024-05-22T08:42:32,094 Created build tracker: /tmp/pip-build-tracker-_na853u_ 2024-05-22T08:42:32,094 Entered build tracker: /tmp/pip-build-tracker-_na853u_ 2024-05-22T08:42:32,095 Created temporary directory: /tmp/pip-wheel-crpk5m96 2024-05-22T08:42:32,099 Created temporary directory: /tmp/pip-ephem-wheel-cache-zkeh6ir4 2024-05-22T08:42:32,123 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-22T08:42:32,126 2 location(s) to search for versions of kssdtree: 2024-05-22T08:42:32,126 * https://pypi.org/simple/kssdtree/ 2024-05-22T08:42:32,126 * https://www.piwheels.org/simple/kssdtree/ 2024-05-22T08:42:32,127 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-05-22T08:42:32,128 Getting page https://pypi.org/simple/kssdtree/ 2024-05-22T08:42:32,129 Found index url https://pypi.org/simple/ 2024-05-22T08:42:32,269 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-05-22T08:42:32,270 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2024-05-22T08:42:32,271 Found link https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.2 2024-05-22T08:42:32,271 Found link https://files.pythonhosted.org/packages/a4/cd/f2954686c636e853cc3fda197c459195377b78288874cf7d68218a8bdbf4/kssdtree-1.1.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.3 2024-05-22T08:42:32,271 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-05-22T08:42:32,272 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-05-22T08:42:32,273 Found index url https://www.piwheels.org/simple/ 2024-05-22T08:42:32,602 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-05-22T08:42:32,605 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv6l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,606 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv7l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,606 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv6l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,606 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv7l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,606 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,607 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,607 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,607 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,607 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv6l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,607 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-05-22T08:42:32,607 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-05-22T08:42:32,608 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-05-22T08:42:32,627 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-05-22T08:42:32,643 Collecting kssdtree==1.1.2 2024-05-22T08:42:32,646 Created temporary directory: /tmp/pip-unpack-1a434776 2024-05-22T08:42:32,690 Downloading kssdtree-1.1.2.tar.gz (113 kB) 2024-05-22T08:42:33,210 Added kssdtree==1.1.2 from https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-_na853u_' 2024-05-22T08:42:33,212 Running setup.py (path:/tmp/pip-wheel-crpk5m96/kssdtree_66406e98aad84d508b47eeaa3f79895f/setup.py) egg_info for package kssdtree 2024-05-22T08:42:33,212 Created temporary directory: /tmp/pip-pip-egg-info-fj1fhyfd 2024-05-22T08:42:33,213 Preparing metadata (setup.py): started 2024-05-22T08:42:33,214 Running command python setup.py egg_info 2024-05-22T08:42:34,310 running egg_info 2024-05-22T08:42:34,311 creating /tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info 2024-05-22T08:42:34,334 writing /tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/PKG-INFO 2024-05-22T08:42:34,338 writing dependency_links to /tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/dependency_links.txt 2024-05-22T08:42:34,340 writing requirements to /tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/requires.txt 2024-05-22T08:42:34,341 writing top-level names to /tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/top_level.txt 2024-05-22T08:42:34,342 writing manifest file '/tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/SOURCES.txt' 2024-05-22T08:42:34,441 reading manifest file '/tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/SOURCES.txt' 2024-05-22T08:42:34,442 reading manifest template 'MANIFEST.in' 2024-05-22T08:42:34,460 writing manifest file '/tmp/pip-pip-egg-info-fj1fhyfd/kssdtree.egg-info/SOURCES.txt' 2024-05-22T08:42:34,558 Preparing metadata (setup.py): finished with status 'done' 2024-05-22T08:42:34,562 Source in /tmp/pip-wheel-crpk5m96/kssdtree_66406e98aad84d508b47eeaa3f79895f has version 1.1.2, which satisfies requirement kssdtree==1.1.2 from https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz 2024-05-22T08:42:34,563 Removed kssdtree==1.1.2 from https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-_na853u_' 2024-05-22T08:42:34,567 Created temporary directory: /tmp/pip-unpack-50l54z_5 2024-05-22T08:42:34,568 Created temporary directory: /tmp/pip-unpack-tkvviawp 2024-05-22T08:42:34,573 Building wheels for collected packages: kssdtree 2024-05-22T08:42:34,578 Created temporary directory: /tmp/pip-wheel-32h1gtoh 2024-05-22T08:42:34,578 Building wheel for kssdtree (setup.py): started 2024-05-22T08:42:34,579 Destination directory: /tmp/pip-wheel-32h1gtoh 2024-05-22T08:42:34,579 Running command python setup.py bdist_wheel 2024-05-22T08:42:35,666 running bdist_wheel 2024-05-22T08:42:35,758 running build 2024-05-22T08:42:35,758 running build_py 2024-05-22T08:42:35,784 creating build 2024-05-22T08:42:35,785 creating build/lib.linux-armv7l-cpython-39 2024-05-22T08:42:35,786 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-05-22T08:42:35,788 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-05-22T08:42:35,790 running egg_info 2024-05-22T08:42:35,843 writing kssdtree.egg-info/PKG-INFO 2024-05-22T08:42:35,846 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-05-22T08:42:35,848 writing requirements to kssdtree.egg-info/requires.txt 2024-05-22T08:42:35,849 writing top-level names to kssdtree.egg-info/top_level.txt 2024-05-22T08:42:35,875 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-05-22T08:42:35,879 reading manifest template 'MANIFEST.in' 2024-05-22T08:42:35,896 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-05-22T08:42:35,898 running build_ext 2024-05-22T08:42:36,480 building 'kssd' extension 2024-05-22T08:42:36,481 creating build/temp.linux-armv7l-cpython-39 2024-05-22T08:42:36,482 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2024-05-22T08:42:36,652 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-05-22T08:42:36,652 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:36,652 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-05-22T08:42:36,653 | ^ 2024-05-22T08:42:36,655 co2mco.c: In function ‘co2unitllmco’: 2024-05-22T08:42:36,655 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:36,655 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-05-22T08:42:36,656 | ^ 2024-05-22T08:42:37,270 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-05-22T08:42:37,568 command_composite.c: In function ‘get_species_abundance’: 2024-05-22T08:42:37,569 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-05-22T08:42:37,569 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-05-22T08:42:37,569 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,569 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-05-22T08:42:37,569 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-05-22T08:42:37,570 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,570 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:37,570 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-05-22T08:42:37,570 | ^ 2024-05-22T08:42:37,570 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-05-22T08:42:37,570 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-05-22T08:42:37,570 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,571 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:37,571 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-05-22T08:42:37,571 | ^ 2024-05-22T08:42:37,571 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-05-22T08:42:37,571 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-05-22T08:42:37,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,572 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:37,572 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-05-22T08:42:37,572 | ^ 2024-05-22T08:42:37,572 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-05-22T08:42:37,572 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-05-22T08:42:37,572 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,572 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:37,573 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-05-22T08:42:37,573 | ^ 2024-05-22T08:42:37,573 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-05-22T08:42:37,573 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-05-22T08:42:37,573 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,573 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:37,573 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-05-22T08:42:37,573 | ^ 2024-05-22T08:42:37,574 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-05-22T08:42:37,574 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-05-22T08:42:37,574 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:37,811 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-05-22T08:42:38,022 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-05-22T08:42:38,023 command_dist.c:678:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:38,023 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-22T08:42:38,023 | ~~^ 2024-05-22T08:42:38,023 | | 2024-05-22T08:42:38,023 | long unsigned int 2024-05-22T08:42:38,024 | %u 2024-05-22T08:42:38,024 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-22T08:42:38,024 | ~~~~~~~ 2024-05-22T08:42:38,024 | | 2024-05-22T08:42:38,024 | size_t {aka unsigned int} 2024-05-22T08:42:38,024 command_dist.c:678:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:38,024 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-22T08:42:38,024 | ~~^ 2024-05-22T08:42:38,025 | | 2024-05-22T08:42:38,025 | long unsigned int 2024-05-22T08:42:38,025 | %u 2024-05-22T08:42:38,025 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-22T08:42:38,025 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-22T08:42:38,025 | ~~~~~~~~~ 2024-05-22T08:42:38,025 | | 2024-05-22T08:42:38,026 | size_t {aka unsigned int} 2024-05-22T08:42:38,026 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-05-22T08:42:38,026 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-22T08:42:38,026 | ~~^ 2024-05-22T08:42:38,026 | | 2024-05-22T08:42:38,026 | long unsigned int 2024-05-22T08:42:38,026 | %u 2024-05-22T08:42:38,027 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-22T08:42:38,027 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-22T08:42:38,027 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:38,027 | | 2024-05-22T08:42:38,027 | unsigned int 2024-05-22T08:42:38,028 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-05-22T08:42:38,028 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-05-22T08:42:38,028 | ^ 2024-05-22T08:42:38,034 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-05-22T08:42:38,035 command_dist.c:864:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:38,035 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-05-22T08:42:38,035 | ~~^ ~~~~~~~ 2024-05-22T08:42:38,036 | | | 2024-05-22T08:42:38,036 | long unsigned int size_t {aka unsigned int} 2024-05-22T08:42:38,036 | %u 2024-05-22T08:42:38,037 command_dist.c:864:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:38,037 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-05-22T08:42:38,037 | ~~^ 2024-05-22T08:42:38,037 | | 2024-05-22T08:42:38,037 | long unsigned int 2024-05-22T08:42:38,037 | %u 2024-05-22T08:42:38,037 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-05-22T08:42:38,038 | ~~~~~~~~~ 2024-05-22T08:42:38,038 | | 2024-05-22T08:42:38,038 | size_t {aka unsigned int} 2024-05-22T08:42:38,038 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-05-22T08:42:38,038 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-05-22T08:42:38,038 | ~~^ 2024-05-22T08:42:38,039 | | 2024-05-22T08:42:38,039 | long unsigned int 2024-05-22T08:42:38,039 | %u 2024-05-22T08:42:38,039 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-05-22T08:42:38,039 866 | (size_t) b * unitsz_distf_mapped); 2024-05-22T08:42:38,039 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:38,039 | | 2024-05-22T08:42:38,040 | unsigned int 2024-05-22T08:42:38,040 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-05-22T08:42:38,040 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-05-22T08:42:38,041 | ^~~~~~~ 2024-05-22T08:42:38,041 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-05-22T08:42:38,041 810 | struct stat cbd_fcode_stat; 2024-05-22T08:42:38,041 | ^~~~~~~~~~~~~~ 2024-05-22T08:42:38,041 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-05-22T08:42:38,041 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-05-22T08:42:38,042 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:38,042 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-05-22T08:42:38,042 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-05-22T08:42:38,042 | ^~~~~~~~~~~~~~~~~ 2024-05-22T08:42:38,048 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-05-22T08:42:38,049 command_dist.c:1019:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:38,049 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-22T08:42:38,049 | ~~^ 2024-05-22T08:42:38,049 | | 2024-05-22T08:42:38,049 | long unsigned int 2024-05-22T08:42:38,049 | %u 2024-05-22T08:42:38,050 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-22T08:42:38,050 | ~~~~~~~ 2024-05-22T08:42:38,050 | | 2024-05-22T08:42:38,050 | size_t {aka unsigned int} 2024-05-22T08:42:38,051 command_dist.c:1019:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:38,051 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-22T08:42:38,051 | ~~^ 2024-05-22T08:42:38,051 | | 2024-05-22T08:42:38,051 | long unsigned int 2024-05-22T08:42:38,051 | %u 2024-05-22T08:42:38,051 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-22T08:42:38,051 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-22T08:42:38,052 | ~~~~~~~~~ 2024-05-22T08:42:38,052 | | 2024-05-22T08:42:38,052 | size_t {aka unsigned int} 2024-05-22T08:42:38,052 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-05-22T08:42:38,052 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-22T08:42:38,053 | ~~^ 2024-05-22T08:42:38,053 | | 2024-05-22T08:42:38,053 | long unsigned int 2024-05-22T08:42:38,053 | %u 2024-05-22T08:42:38,053 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-22T08:42:38,053 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-22T08:42:38,053 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:38,054 | | 2024-05-22T08:42:38,054 | unsigned int 2024-05-22T08:42:38,054 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,054 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-05-22T08:42:38,054 | ^ 2024-05-22T08:42:38,057 command_dist.c: In function ‘mco_co_dist_core’: 2024-05-22T08:42:38,058 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-05-22T08:42:38,058 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-05-22T08:42:38,058 | ^ 2024-05-22T08:42:38,064 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-05-22T08:42:38,064 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,064 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-05-22T08:42:38,065 | ^ 2024-05-22T08:42:38,066 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,066 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-05-22T08:42:38,066 | ^ 2024-05-22T08:42:38,071 command_dist.c: In function ‘dist_print_nobin’: 2024-05-22T08:42:38,072 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,072 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-05-22T08:42:38,072 | ^ 2024-05-22T08:42:38,074 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,074 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-05-22T08:42:38,074 | ^ 2024-05-22T08:42:38,076 command_dist.c:1381:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,076 1381 | for (int rid = 0; rid < ref_num; rid++) 2024-05-22T08:42:38,076 | ^ 2024-05-22T08:42:38,076 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:38,077 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-05-22T08:42:38,077 | ^ 2024-05-22T08:42:38,327 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-05-22T08:42:38,328 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-22T08:42:38,328 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-05-22T08:42:38,328 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:38,328 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-05-22T08:42:38,328 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-05-22T08:42:38,328 | ^~~~~~~~~~~~ 2024-05-22T08:42:39,049 command_dist.c: In function ‘get_dim_shuffle’: 2024-05-22T08:42:39,049 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-05-22T08:42:39,049 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-05-22T08:42:39,049 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:39,049 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-05-22T08:42:39,050 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-05-22T08:42:39,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:39,830 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-05-22T08:42:39,831 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:39,831 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-22T08:42:39,831 | ^~ ~~~~~~~~~ 2024-05-22T08:42:39,831 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-05-22T08:42:39,831 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-22T08:42:39,831 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:39,832 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:39,832 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-22T08:42:39,832 | ^~~~~~~~~~~~~~~ 2024-05-22T08:42:39,832 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-05-22T08:42:39,832 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-22T08:42:39,832 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:39,833 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:39,834 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-22T08:42:39,834 | ^~~~~~~~~~~ 2024-05-22T08:42:39,834 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-05-22T08:42:39,834 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-22T08:42:39,834 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:39,834 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:39,834 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-22T08:42:39,835 | ^~~~~ 2024-05-22T08:42:39,835 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-22T08:42:39,835 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-22T08:42:39,835 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,040 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-05-22T08:42:40,041 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:40,041 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-22T08:42:40,041 | ^~ ~~~~~~~~~ 2024-05-22T08:42:40,042 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-05-22T08:42:40,042 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-22T08:42:40,042 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,042 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:40,043 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-22T08:42:40,043 | ^~~~~~~~~~~~~~~ 2024-05-22T08:42:40,043 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-05-22T08:42:40,043 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-22T08:42:40,043 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,044 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:40,044 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-22T08:42:40,044 | ^~~~~~~~~~~~~ 2024-05-22T08:42:40,044 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-05-22T08:42:40,044 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-22T08:42:40,045 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,045 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:40,046 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-05-22T08:42:40,046 | ^ 2024-05-22T08:42:40,046 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-05-22T08:42:40,046 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-05-22T08:42:40,046 | ^~~~~~~~~~ 2024-05-22T08:42:40,047 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-05-22T08:42:40,047 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-05-22T08:42:40,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,047 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:40,047 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-05-22T08:42:40,048 | ^ 2024-05-22T08:42:40,048 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-05-22T08:42:40,048 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-05-22T08:42:40,048 | ^~~~~~~~~~ 2024-05-22T08:42:40,048 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-05-22T08:42:40,049 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-05-22T08:42:40,049 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,285 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-05-22T08:42:40,286 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:40,286 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-22T08:42:40,286 | ^~ ~~~~~~~~~ 2024-05-22T08:42:40,287 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-05-22T08:42:40,287 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-22T08:42:40,287 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,287 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:40,288 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-22T08:42:40,288 | ^~~~~~~~~~~~~~~ 2024-05-22T08:42:40,288 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-05-22T08:42:40,288 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-22T08:42:40,288 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,289 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:40,289 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-22T08:42:40,289 | ^~~~~~~~~~~~~ 2024-05-22T08:42:40,290 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-05-22T08:42:40,290 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-22T08:42:40,290 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,291 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:40,291 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-22T08:42:40,291 | ^~~~~~~~~~~ 2024-05-22T08:42:40,292 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-05-22T08:42:40,292 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-22T08:42:40,292 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,293 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-22T08:42:40,293 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-22T08:42:40,293 | ^~~~~ 2024-05-22T08:42:40,293 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-22T08:42:40,293 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-22T08:42:40,293 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,539 command_dist.c: In function ‘combine_queries’: 2024-05-22T08:42:40,540 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:40,540 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-05-22T08:42:40,540 | ^ 2024-05-22T08:42:40,541 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:40,541 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-05-22T08:42:40,541 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,542 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:40,542 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-05-22T08:42:40,542 | ^ 2024-05-22T08:42:40,543 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:40,543 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-05-22T08:42:40,543 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:40,545 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:40,546 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-05-22T08:42:40,546 | ^~ ~~~~~~~~ 2024-05-22T08:42:40,546 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-05-22T08:42:40,547 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-05-22T08:42:40,547 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,023 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2024-05-22T08:42:41,189 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2024-05-22T08:42:41,334 command_set.c: In function ‘sketch_operate’: 2024-05-22T08:42:41,334 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-05-22T08:42:41,334 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-05-22T08:42:41,334 | ^ 2024-05-22T08:42:41,344 command_set.c: In function ‘combin_subset_pans’: 2024-05-22T08:42:41,344 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-05-22T08:42:41,344 458 | free(co_dstat_fpath); 2024-05-22T08:42:41,344 | ^~~~~~~~~~~~~~ 2024-05-22T08:42:41,345 In file included from kssdheaders/global_basic.h:159, 2024-05-22T08:42:41,345 from command_set.c:15: 2024-05-22T08:42:41,345 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-05-22T08:42:41,345 565 | extern void free (void *__ptr) __THROW; 2024-05-22T08:42:41,345 | ~~~~~~^~~~~ 2024-05-22T08:42:41,349 command_set.c: In function ‘grouping_genomes’: 2024-05-22T08:42:41,349 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-05-22T08:42:41,350 563 | free(co_dstat_fpath); 2024-05-22T08:42:41,350 | ^~~~~~~~~~~~~~ 2024-05-22T08:42:41,350 In file included from kssdheaders/global_basic.h:159, 2024-05-22T08:42:41,350 from command_set.c:15: 2024-05-22T08:42:41,350 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-05-22T08:42:41,350 565 | extern void free (void *__ptr) __THROW; 2024-05-22T08:42:41,351 | ~~~~~~^~~~~ 2024-05-22T08:42:41,465 command_set.c: In function ‘sketch_union’: 2024-05-22T08:42:41,466 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:41,466 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,466 | ^ 2024-05-22T08:42:41,466 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:41,466 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,466 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,466 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,467 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-22T08:42:41,467 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,467 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:41,467 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-22T08:42:41,467 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,467 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,467 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-05-22T08:42:41,468 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:41,468 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-22T08:42:41,468 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-05-22T08:42:41,468 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,579 command_set.c: In function ‘sketch_operate’: 2024-05-22T08:42:41,579 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,580 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-05-22T08:42:41,580 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:41,580 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-22T08:42:41,580 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-05-22T08:42:41,580 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,580 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,580 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-05-22T08:42:41,581 | ^~ ~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,581 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-05-22T08:42:41,581 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-05-22T08:42:41,581 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,581 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,581 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-22T08:42:41,581 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,581 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-22T08:42:41,582 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-22T08:42:41,582 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,582 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,582 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-22T08:42:41,582 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,582 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:41,582 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-22T08:42:41,583 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,583 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,583 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-05-22T08:42:41,583 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,583 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:41,583 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-05-22T08:42:41,583 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,583 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,584 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-05-22T08:42:41,584 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,584 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-22T08:42:41,584 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-05-22T08:42:41,584 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,584 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:41,584 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,585 | ^ 2024-05-22T08:42:41,585 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:41,585 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,585 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,732 command_set.c: In function ‘uniq_sketch_union’: 2024-05-22T08:42:41,733 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:41,733 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,733 | ^ 2024-05-22T08:42:41,733 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:41,733 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,733 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,734 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-22T08:42:41,734 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,734 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:41,734 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-22T08:42:41,734 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,734 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,734 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-05-22T08:42:41,735 | ^~ ~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,735 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-05-22T08:42:41,735 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-05-22T08:42:41,735 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,859 command_set.c: In function ‘combin_pans’: 2024-05-22T08:42:41,859 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,859 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:41,860 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:41,860 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-05-22T08:42:41,860 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:41,860 | ^~~~~~~~~~ 2024-05-22T08:42:41,860 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-05-22T08:42:41,860 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:41,860 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,860 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:41,861 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:41,861 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:41,861 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-05-22T08:42:41,861 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:41,861 | ^~~~~~~~~~ 2024-05-22T08:42:41,861 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-05-22T08:42:41,861 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:41,861 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:41,862 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:41,862 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,862 | ^ 2024-05-22T08:42:41,862 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:41,862 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:41,862 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,045 command_set.c: In function ‘combin_subset_pans’: 2024-05-22T08:42:42,045 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,045 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-22T08:42:42,045 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:42,046 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:42,046 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-22T08:42:42,046 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,046 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,046 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-22T08:42:42,046 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:42,046 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-22T08:42:42,047 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-22T08:42:42,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,047 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,047 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:42,047 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:42,047 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:42,047 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:42,048 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,049 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,049 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:42,049 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:42,049 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-22T08:42:42,049 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:42,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,050 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:42,050 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:42,050 | ^ 2024-05-22T08:42:42,050 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:42,050 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:42,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,251 command_set.c: In function ‘grouping_genomes’: 2024-05-22T08:42:42,252 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,252 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-22T08:42:42,252 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:42,252 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:42,252 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-22T08:42:42,252 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,253 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,253 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-22T08:42:42,253 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:42,253 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-22T08:42:42,253 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-22T08:42:42,253 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,255 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,255 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:42,255 | ^~ ~~~~~~~~~~~ 2024-05-22T08:42:42,256 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-22T08:42:42,256 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-22T08:42:42,256 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,257 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-22T08:42:42,257 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:42,257 | ^~ ~~~~~~~~~~ 2024-05-22T08:42:42,257 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-22T08:42:42,257 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-22T08:42:42,257 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,258 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-22T08:42:42,258 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:42,258 | ^ 2024-05-22T08:42:42,258 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-22T08:42:42,258 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-22T08:42:42,258 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:42,529 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2024-05-22T08:42:42,808 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2024-05-22T08:42:43,032 global_basic.c: In function ‘organize_infile_list’: 2024-05-22T08:42:43,033 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-05-22T08:42:43,033 195 | while (isspace(*buf)) buf++; 2024-05-22T08:42:43,033 | ^~~~~~~ 2024-05-22T08:42:43,033 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:43,033 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-05-22T08:42:43,033 | ~~^ 2024-05-22T08:42:43,034 | | 2024-05-22T08:42:43,034 | long unsigned int 2024-05-22T08:42:43,034 | %u 2024-05-22T08:42:43,034 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-05-22T08:42:43,034 | ~~~~~~~~~~~ 2024-05-22T08:42:43,034 | | 2024-05-22T08:42:43,034 | size_t {aka unsigned int} 2024-05-22T08:42:43,035 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-22T08:42:43,035 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-05-22T08:42:43,035 | ~~^ 2024-05-22T08:42:43,035 | | 2024-05-22T08:42:43,035 | long unsigned int 2024-05-22T08:42:43,035 | %u 2024-05-22T08:42:43,036 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-05-22T08:42:43,036 | ~~~~~~~~~~~ 2024-05-22T08:42:43,036 | | 2024-05-22T08:42:43,036 | size_t {aka unsigned int} 2024-05-22T08:42:43,712 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2024-05-22T08:42:43,887 iseq2comem.c: In function ‘reads2mco’: 2024-05-22T08:42:43,887 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,888 156 | if (base > TL) { 2024-05-22T08:42:43,888 | ^ 2024-05-22T08:42:43,888 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,888 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,888 | ^~ 2024-05-22T08:42:43,888 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,889 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,889 | ^ 2024-05-22T08:42:43,889 iseq2comem.c: In function ‘fasta2co’: 2024-05-22T08:42:43,890 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,890 239 | if (base > TL) { 2024-05-22T08:42:43,890 | ^ 2024-05-22T08:42:43,890 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,890 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,890 | ^~ 2024-05-22T08:42:43,891 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,891 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,891 | ^ 2024-05-22T08:42:43,891 iseq2comem.c: In function ‘fastq2co’: 2024-05-22T08:42:43,891 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-05-22T08:42:43,891 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-05-22T08:42:43,891 | ^~ 2024-05-22T08:42:43,892 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,892 318 | if (base > TL) { 2024-05-22T08:42:43,893 | ^ 2024-05-22T08:42:43,893 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,893 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,893 | ^~ 2024-05-22T08:42:43,893 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,893 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,893 | ^ 2024-05-22T08:42:43,894 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,894 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-05-22T08:42:43,894 | ^ 2024-05-22T08:42:43,895 iseq2comem.c: In function ‘fastq2koc’: 2024-05-22T08:42:43,895 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,896 402 | if (base > TL) { 2024-05-22T08:42:43,896 | ^ 2024-05-22T08:42:43,896 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,896 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,896 | ^~ 2024-05-22T08:42:43,896 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,896 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,897 | ^ 2024-05-22T08:42:43,902 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-05-22T08:42:43,902 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,902 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,902 | ^~ 2024-05-22T08:42:43,902 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:43,902 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-22T08:42:43,903 | ^ 2024-05-22T08:42:45,063 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-05-22T08:42:45,127 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2024-05-22T08:42:45,248 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-05-22T08:42:45,561 pykssd.c: In function ‘py_dist_dispatch’: 2024-05-22T08:42:45,561 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-05-22T08:42:45,562 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-05-22T08:42:45,562 | ^~~~~~ 2024-05-22T08:42:45,563 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-05-22T08:42:45,563 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-05-22T08:42:45,563 | ^~~~~~ 2024-05-22T08:42:45,565 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-05-22T08:42:45,565 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-05-22T08:42:45,565 | ^~~~~~ 2024-05-22T08:42:45,703 pykssd.c: In function ‘rename_file’: 2024-05-22T08:42:45,703 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-05-22T08:42:45,703 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-05-22T08:42:45,704 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-22T08:42:45,704 pykssd.c:41:15: note: length computed here 2024-05-22T08:42:45,704 41 | int len = strlen(p1); 2024-05-22T08:42:45,704 | ^~~~~~~~~~ 2024-05-22T08:42:46,068 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-05-22T08:42:46,227 building 'nj' extension 2024-05-22T08:42:46,228 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c align.c -o build/temp.linux-armv7l-cpython-39/align.o 2024-05-22T08:42:46,739 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c buildtree.c -o build/temp.linux-armv7l-cpython-39/buildtree.o 2024-05-22T08:42:46,869 buildtree.c: In function ‘UPGMA_buildtree’: 2024-05-22T08:42:46,869 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:46,870 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-05-22T08:42:46,870 | ^~ 2024-05-22T08:42:46,870 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:46,871 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-05-22T08:42:46,871 | ^~ 2024-05-22T08:42:47,438 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c cluster.c -o build/temp.linux-armv7l-cpython-39/cluster.o 2024-05-22T08:42:47,758 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c distancemat.c -o build/temp.linux-armv7l-cpython-39/distancemat.o 2024-05-22T08:42:47,878 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-05-22T08:42:47,878 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:47,878 226 | for( i=0; i < dest->size; i++) { 2024-05-22T08:42:47,878 | ^ 2024-05-22T08:42:47,879 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-05-22T08:42:47,879 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:47,879 260 | for( i=0; i < mat->size; i++) { 2024-05-22T08:42:47,879 | ^ 2024-05-22T08:42:47,880 distancemat.c: In function ‘print_DistanceMatrix’: 2024-05-22T08:42:47,881 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:47,881 349 | for(row=0; row < mat->size; row++) { 2024-05-22T08:42:47,881 | ^ 2024-05-22T08:42:47,882 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-05-22T08:42:47,883 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-05-22T08:42:47,883 410 | while(c = fgetc(handle)) { 2024-05-22T08:42:47,883 | ^ 2024-05-22T08:42:48,250 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2024-05-22T08:42:48,624 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c sequence.c -o build/temp.linux-armv7l-cpython-39/sequence.o 2024-05-22T08:42:48,837 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c tree.c -o build/temp.linux-armv7l-cpython-39/tree.o 2024-05-22T08:42:49,563 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c util.c -o build/temp.linux-armv7l-cpython-39/util.o 2024-05-22T08:42:49,736 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/align.o build/temp.linux-armv7l-cpython-39/buildtree.o build/temp.linux-armv7l-cpython-39/cluster.o build/temp.linux-armv7l-cpython-39/distancemat.o build/temp.linux-armv7l-cpython-39/pynj.o build/temp.linux-armv7l-cpython-39/sequence.o build/temp.linux-armv7l-cpython-39/tree.o build/temp.linux-armv7l-cpython-39/util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so 2024-05-22T08:42:49,852 building 'dnj' extension 2024-05-22T08:42:49,853 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c bytescale.c -o build/temp.linux-armv7l-cpython-39/bytescale.o -fopenmp 2024-05-22T08:42:49,921 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c dnj.c -o build/temp.linux-armv7l-cpython-39/dnj.o -fopenmp 2024-05-22T08:42:50,044 dnj.c: In function ‘minQpair’: 2024-05-22T08:42:50,045 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,045 70 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,045 | ^~~ 2024-05-22T08:42:50,046 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,046 126 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,046 | ^~~ 2024-05-22T08:42:50,046 dnj.c: In function ‘maxQpair’: 2024-05-22T08:42:50,047 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,047 157 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,047 | ^~~ 2024-05-22T08:42:50,047 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,047 213 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,048 | ^~~ 2024-05-22T08:42:50,048 dnj.c: In function ‘UPGMApair’: 2024-05-22T08:42:50,048 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,048 237 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,048 | ^~~ 2024-05-22T08:42:50,049 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,049 284 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,049 | ^~~ 2024-05-22T08:42:50,049 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,049 291 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,049 | ^~~ 2024-05-22T08:42:50,050 dnj.c: In function ‘minQrow’: 2024-05-22T08:42:50,050 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,051 374 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,051 | ^~~ 2024-05-22T08:42:50,051 dnj.c: In function ‘maxQrow’: 2024-05-22T08:42:50,052 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,052 435 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,052 | ^~~ 2024-05-22T08:42:50,053 dnj.c: In function ‘UPGMArow’: 2024-05-22T08:42:50,053 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,053 488 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,053 | ^~~ 2024-05-22T08:42:50,053 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,053 494 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,054 | ^~~ 2024-05-22T08:42:50,054 dnj.c: In function ‘minQ_thread’: 2024-05-22T08:42:50,055 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:50,055 553 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:50,055 | ^~~ 2024-05-22T08:42:51,218 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2024-05-22T08:42:51,324 filebuff.c: In function ‘BuffgzFileBuff’: 2024-05-22T08:42:51,324 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:51,325 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-05-22T08:42:51,325 | ^~ 2024-05-22T08:42:51,608 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c hclust.c -o build/temp.linux-armv7l-cpython-39/hclust.o -fopenmp 2024-05-22T08:42:51,727 hclust.c: In function ‘minQ’: 2024-05-22T08:42:51,728 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:51,728 364 | while(++i < Q->n) { 2024-05-22T08:42:51,728 | ^ 2024-05-22T08:42:51,728 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:51,728 377 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:51,728 | ^~~ 2024-05-22T08:42:51,729 hclust.c: In function ‘maxQ’: 2024-05-22T08:42:51,729 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-22T08:42:51,729 394 | while(++i < Q->n) { 2024-05-22T08:42:51,729 | ^ 2024-05-22T08:42:51,729 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:51,729 407 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:51,729 | ^~~ 2024-05-22T08:42:53,804 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2024-05-22T08:42:53,927 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-05-22T08:42:53,927 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-22T08:42:53,927 538 | if(pos != n) { 2024-05-22T08:42:53,928 | ^~ 2024-05-22T08:42:54,678 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-05-22T08:42:54,741 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nj.c -o build/temp.linux-armv7l-cpython-39/nj.o -fopenmp 2024-05-22T08:42:54,856 nj.c: In function ‘initQ’: 2024-05-22T08:42:54,856 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:54,856 243 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:54,856 | ^~~ 2024-05-22T08:42:54,858 nj.c: In function ‘initQ_MN’: 2024-05-22T08:42:54,859 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:54,859 358 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:54,859 | ^~~ 2024-05-22T08:42:54,863 nj.c: In function ‘minD’: 2024-05-22T08:42:54,863 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:54,863 559 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:54,863 | ^~~ 2024-05-22T08:42:54,866 nj.c: In function ‘maxD’: 2024-05-22T08:42:54,866 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:54,866 642 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:54,866 | ^~~ 2024-05-22T08:42:54,870 nj.c: In function ‘minPair’: 2024-05-22T08:42:54,871 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-22T08:42:54,871 826 | pos <<= sizeof(unsigned) * 8; 2024-05-22T08:42:54,871 | ^~~ 2024-05-22T08:42:56,946 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nwck.c -o build/temp.linux-armv7l-cpython-39/nwck.o -fopenmp 2024-05-22T08:42:57,412 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pherror.c -o build/temp.linux-armv7l-cpython-39/pherror.o -fopenmp 2024-05-22T08:42:57,499 pherror.c: In function ‘cfread’: 2024-05-22T08:42:57,499 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-22T08:42:57,500 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-05-22T08:42:57,500 | ^~ 2024-05-22T08:42:57,590 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c phy.c -o build/temp.linux-armv7l-cpython-39/phy.o -fopenmp 2024-05-22T08:42:58,506 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2024-05-22T08:42:58,830 In file included from pydnj.c:11: 2024-05-22T08:42:58,830 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-05-22T08:42:58,830 20 | #define _XOPEN_SOURCE 600 2024-05-22T08:42:58,830 | 2024-05-22T08:42:58,830 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-05-22T08:42:58,831 from /usr/include/limits.h:26, 2024-05-22T08:42:58,831 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-05-22T08:42:58,831 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-05-22T08:42:58,831 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-05-22T08:42:58,831 from /usr/include/python3.9/Python.h:11, 2024-05-22T08:42:58,831 from pydnj.c:1: 2024-05-22T08:42:58,832 /usr/include/features.h:207: note: this is the location of the previous definition 2024-05-22T08:42:58,832 207 | # define _XOPEN_SOURCE 700 2024-05-22T08:42:58,832 | 2024-05-22T08:42:58,845 pydnj.c: In function ‘py_build’: 2024-05-22T08:42:58,846 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-05-22T08:42:58,846 165 | p = omp_get_num_procs(); 2024-05-22T08:42:58,846 | ^~~~~~~~~~~~~~~~~ 2024-05-22T08:42:59,026 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c qseqs.c -o build/temp.linux-armv7l-cpython-39/qseqs.o -fopenmp 2024-05-22T08:42:59,215 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c str.c -o build/temp.linux-armv7l-cpython-39/str.o -fopenmp 2024-05-22T08:42:59,324 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c tmp.c -o build/temp.linux-armv7l-cpython-39/tmp.o -fopenmp 2024-05-22T08:42:59,511 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c vector.c -o build/temp.linux-armv7l-cpython-39/vector.o -fopenmp 2024-05-22T08:42:59,664 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/bytescale.o build/temp.linux-armv7l-cpython-39/dnj.o build/temp.linux-armv7l-cpython-39/filebuff.o build/temp.linux-armv7l-cpython-39/hclust.o build/temp.linux-armv7l-cpython-39/matrix.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/nj.o build/temp.linux-armv7l-cpython-39/nwck.o build/temp.linux-armv7l-cpython-39/pherror.o build/temp.linux-armv7l-cpython-39/phy.o build/temp.linux-armv7l-cpython-39/pydnj.o build/temp.linux-armv7l-cpython-39/qseqs.o build/temp.linux-armv7l-cpython-39/str.o build/temp.linux-armv7l-cpython-39/tmp.o build/temp.linux-armv7l-cpython-39/vector.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-05-22T08:42:59,865 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-05-22T08:42:59,865 !! 2024-05-22T08:42:59,866 ******************************************************************************** 2024-05-22T08:42:59,866 Please avoid running ``setup.py`` directly. 2024-05-22T08:42:59,866 Instead, use pypa/build, pypa/installer or other 2024-05-22T08:42:59,866 standards-based tools. 2024-05-22T08:42:59,866 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-05-22T08:42:59,866 ******************************************************************************** 2024-05-22T08:42:59,867 !! 2024-05-22T08:42:59,867 self.initialize_options() 2024-05-22T08:42:59,888 installing to build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,889 running install 2024-05-22T08:42:59,914 running install_lib 2024-05-22T08:42:59,938 creating build/bdist.linux-armv7l 2024-05-22T08:42:59,939 creating build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,940 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,943 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,948 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,962 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,964 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-05-22T08:42:59,977 running install_egg_info 2024-05-22T08:43:00,009 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.2-py3.9.egg-info 2024-05-22T08:43:00,020 running install_scripts 2024-05-22T08:43:00,038 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.2.dist-info/WHEEL 2024-05-22T08:43:00,040 creating '/tmp/pip-wheel-32h1gtoh/kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-22T08:43:00,119 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-05-22T08:43:00,213 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-05-22T08:43:00,218 adding 'kssdtree.py' 2024-05-22T08:43:00,239 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-05-22T08:43:00,242 adding 'toolutils.py' 2024-05-22T08:43:00,244 adding 'kssdtree-1.1.2.dist-info/METADATA' 2024-05-22T08:43:00,245 adding 'kssdtree-1.1.2.dist-info/WHEEL' 2024-05-22T08:43:00,246 adding 'kssdtree-1.1.2.dist-info/dependency_links.txt' 2024-05-22T08:43:00,247 adding 'kssdtree-1.1.2.dist-info/top_level.txt' 2024-05-22T08:43:00,248 adding 'kssdtree-1.1.2.dist-info/RECORD' 2024-05-22T08:43:00,253 removing build/bdist.linux-armv7l/wheel 2024-05-22T08:43:00,392 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-05-22T08:43:00,399 Created wheel for kssdtree: filename=kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl size=375680 sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db 2024-05-22T08:43:00,400 Stored in directory: /tmp/pip-ephem-wheel-cache-zkeh6ir4/wheels/57/21/88/ec8973f1c57f6fc17de7a76658617fd334f9f8b804447414af 2024-05-22T08:43:00,411 Successfully built kssdtree 2024-05-22T08:43:00,424 Removed build tracker: '/tmp/pip-build-tracker-_na853u_'